Authorities advised thousands living in coastal areas or near rivers to evacuate to shelters before Typhoon Lan, described as "very large and very strong", hit Tokyo and surrounding regions early Monday morning.
The typhoon had left the Japanese archipelago by about 9:00 am after making landfall in Shizuoka southwest of Tokyo six hours before, the weather agency said.
The storm, which had already dumped torrential rain over much of the country during the weekend, packed gusts up to 162 kilometres per hour, the meteorological agency said.
Nearly 300 flights scheduled for Monday have already been cancelled, public broadcaster NHK said, after strong winds forced 500 flights to be grounded Sunday.
Some ferry services in western Japan were also cancelled as the weather agency warned of high waves, landslides and floods across the archipelago.
The typhoon claimed its first victims Sunday as a male passer-by died when scaffolding collapsed on him at a construction site in Fukuoka in western Japan.
In Osaka prefecture, a man in his 80s died after being crushed under a blown-off shutter while a woman in her 60s was found dead in a submerged car, local officials said.
A 29-year-old man was also found in a submerged car in the central prefecture of Mie.
Separately, a 61-year-old man has been missing in eastern Japan's Ibaraki prefecture after he went fishing on Sunday.
Television footage showed rescuers tugging a rubber boat carrying an elderly woman in a residential area in Chiba southeast of Tokyo as a flooded river engulfed the area.
Automaker Toyota said it would suspend operations at all domestic plants today.
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